I wish to show coverage information from two different places in the genome at the same time. Using a grid and plotting two AlignmentsTracks next to each other works well, but I would like the y-axis limit to be the same in each of the two subplots. I know I can do this by using the ylim-parameter, but then I have to know the range in advance. I would like to make it work so that it takes the biggest range of subplotA and subplotB and applies it to both. If there a way to check in advance what the ylim parameter should be set to?

Hm, not really. You would have to tease apart your data before the plotting. The individual plotTracks() calls are totaly independent